Differences between revisions 13 and 29 (spanning 16 versions)

Enrichment Map Gene Sets

Contents

Enrichment Map Gene Sets

Summary

Gene Set Files can be downloaded from : http://download.baderlab.org/EM_Genesets/
Enrichment Map Gene Sets are a set of Gene Set files in GMT format (compatible with GSEA) updated monthly from original source locations available with:
1. Entrez gene ids
2. UniProt accessions
3. Gene symbols
The GMT File format contains one Gene Set per line. Each line contains:
- Name (tab) Description (tab) Gene (tab) Gene (tab) ...
- In our format:
  - Name = Gene Set Name | Gene Set Source | Gene Set Source identifier
    - Example --> ATP-dependent protein binding|GO|GO:0043008 OR arginine biosynthesis IV|HUMANCYC|ARGININE-SYN4-PWY
  - Description = Gene Set Name
    - Example --> ATP-dependent protein binding OR arginine biosynthesis IV
  - Gene = identified by one of the three possible identifiers (Entrez gene id, UniProt accession or gene symbols)

Sources

Human

Source	File Origin	File Type	ID extracted	Frequency source is updated	Number of pathways
KEGG^[[#ref1\|1]]	KEGG ftp site (July 2011)	GMT	Symbol	static as of July 1, 2011	236
Msigdb - c2^[[#ref2\|2]] (other + Biocarta)	manual download from Msigdb	GMT	Entrez gene	sporadically	Biocarta - 217 Other - 47
NCI^[[#ref3\|3]]	scripted download of zipped release from website	BioPAX	Entrez gene	sporadically	219 pathways
IOB	received directly from IOB - static (July 2011)	BioPAX	Entrez gene	sporadically	35 pathways - 10 are the same as CellMap, 1 is the same as NetPath
NetPath^[[#ref4\|4]]	scripted download of files numbered 1-25	BioPAX	Entrez gene	static	25 pathways - 12 are cancer pathways (10 are CellMap) 13 are immunity pathways
HumanCyc^[[#ref5\|5]]	scripted download of zipped release from password protected website.	BioPAX	UniProt	updated periodically	249 Pathways
Reactome^[[#ref6\|6]]	scripted download of zipped release from website	BioPAX	UniProt	updated release	1117 pathways (release 37)
GO^[[#ref7\|7]]	scripted download from EBI ftp site (human)	GAF	Uniprot	released once a month	13,034 no GO IEA 15,181 with GO IEA
Msigdb - c3^[[#ref2\|2]] Specialty GMTs mirs, transcription factors	manual download from Msigdb	GMT	Entrez gene	sporadically	221 miRs 616 TFs

Mouse

Source	File Origin	File Type	ID extracted	Frequency source is updated	Number of pathways
Reactome^[[#ref6\|6]]	scripted download of zipped release from website	BioPAX	UniProt	updated release	946 pathways (release 37)
GO^[[#ref7\|7]]	scripted download from MGI ftp site (mouse)	GAF	MGI	released once a month	14,563 no GO IEA 15,041 with GO IEA
KEGG¹	translated from Human using Homologene	GMT	Entrez gene	static as of July 1, 2011	236
Msigdb - c2^[[#ref2\|2]] (other + Biocarta)	translated from Human using Homologene	GMT	Entrez gene	sporadically	total 880: Kegg -186 Reactome - 430 Biocarta - 217 Other - 47
NCI^[[#ref3\|3]]	translated from Human using Homologene	GMT	Entrez gene	sporadically	219 pathways
IOB	translated from Human using Homologene	GMT	Entrez gene	sporadically	35 pathways - 10 are the same as CellMap, 1 is the same as NetPath
NetPath^[[#ref4\|4]]	translated from Human using Homologene	GMT	Entrez gene	static	25 pathways - 12 are cancer pathways (10 are CellMap) 13 are immunity pathways
HumanCyc^[[#ref5\|5]]	translated from Human using Homologene	GMT	Entrez gene	updated periodically	249 Pathways

File Structure

< > denotes directory

<Release> - directory is named according to date sets were updated.
- <Species>
  - <Identifier> - (either Entrez gene, UniProt, Gene symbol)
    - <GO>
      - BP = biological process
      - MF = molecular function
      - CC = Cellular component
      - All = BP + MF + CC
      - no_GO_IEA - indicates that the file excludes GO annotations with evidence codes - 'IEA' (inferred from electronic annotation), 'ND' (No biological data available), 'RCA' (inferred from reviewed computational analysis)
      - with_GO_IEA - indicates that the file includes GO annotations with evidence codes - 'IEA' (inferred from electronic annotation), 'ND' (No biological data available), 'RCA' (inferred from reviewed computational analysis)
    - <Pathways>
    - <miRs>
    - <TF>
    - <Disease phenotypes>
In each <identifier> directory There are amalgamated Gene Set files:
- AllPathways - contains all pathway sources in the Pathways directory
- GOPathways - contains all GO (MF, BP, CC) and all Pathway sources in the Pathways directory.

Creating customized Gene Sets

Download the desired gene set files you would like to use in your customized set. (For example Human_IOB_Entrezgene.gmt Human_NetPath_Entrezgene.gmt )

   cat Human_IOB_Entrezgene.gmt Human_NetPath_Entrezgene.gmt > MyCustomizedSet.gmt

References

Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2011 Nov 10. PMID: 22080510
Pubmed

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. PMID: 16199517
Pubmed

Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. PMID: 18832364
Pubmed

Kandasamy K, et a NetPath: a public resource of curated signal transduction pathways.Genome Biol. 2010 Jan 12;11(1):R3. PMID: 20067622 Pubmed

Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 2005;6(1):R2. Epub 2004 Dec 22. PMID: 15642094
Pubmed

Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. Reactome: a database of reactions, pathways and biological processes Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7. PMID: 21067998 Pubmed

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9. PMID: 10802651 Pubmed

-  ⇤ ← Revision 13 as of 2011-10-24 20:38:48 → 
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+   ← Revision 29 as of 2011-11-15 18:46:08 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+## page was renamed from UpToDateGeneSets/EmGeneSetsReadme
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+Line 3:
-= Enrichment Map Genesets =
+= Enrichment Map Gene Sets =
-Line 6:
+Line 7:
-  * Enrichment Map Genesets are a set of Gene Set files in GMT format (compatible with [[http://www.broadinstitute.org/gsea/index.jsp| GSEA]]) updated '''monthly''' from original source locations available with:
+  * Gene Set Files can be downloaded from : [[http://download.baderlab.org/EM_Genesets/]]
  * Enrichment Map Gene Sets are a set of Gene Set files in GMT format (compatible with [[http://www.broadinstitute.org/gsea/index.jsp| GSEA]]) updated '''monthly''' from original source locations available with:
-Line 10:
+Line 12:
+  * The GMT File format contains one Gene Set per line.  Each line contains:
    * Name (tab) Description (tab) Gene (tab) Gene (tab) ...
    * In our format:
      * Name = Gene Set Name | Gene Set Source | Gene Set Source identifier
        * Example --> ATP-dependent protein binding|GO|GO:0043008  '''OR'''    arginine biosynthesis IV|HUMANCYC|ARGININE-SYN4-PWY
      * Description = Gene Set Name
         * Example -->  ATP-dependent protein binding '''OR'''    arginine biosynthesis IV
      * Gene = identified by one of the three possible identifiers (Entrez gene id, !UniProt accession or gene symbols)
-Line 13:
+Line 23:
-|| '''Source''' || '''File Origin''' || '''File Type''' || '''ID extracted''' || '''Frequency source is updated''' ||  '''Number of pathwayss''' || '''Notes''' ||
|| KEGG || KEGG ftp site (July 2011) || gmt || symbol ||  static as of July 1, 2011 || 236 || Not available in biopax, available in flatfile, translated into gmt files ||
|| Msigdb - c2|| static (needs to be updated manually) || gmt || Entrez gene || sporadically ||  Biocarta - 217<<BR>> Other - 47 || Only need other and Biocarta as all other sources are currently covered ||
|| NCI || [[http://pid.nci.nih.gov/download.shtml|NCI]] || biopax || Entrez gene || sporadically || 219 pathways ||   ||
|| {X} Biocarta || [[http://pid.nci.nih.gov/download.shtml|NCI]] || biopax || Entrez gene || static || 386 pathways || '''Biopax 3 - Complete Mess!''' - currently getting from Msigdb ||
|| IOB || directly from IOB - static (July 2011) || biopax || Entrez gene || sporadically  || 35 pathways -  <<BR>> 10 are the same as !CellMap,<<BR>> 1 is the same as !NetPath|| need biopax pathways fixed so species info is correct but information is still extractable. ||
|| !NetPath || [[www.netpath.org/browse]] (scripted grab of file numbered 1-25) || biopax || Entrez gene || static ||  25 pathways - <<BR>> 12 are cancer pathways (10 are !CellMap) <<BR>> 13 are immunity pathways || need biopax pathways fixed so species info is correct but information is still extractable. ||
|| !HumanCyc || scripted grab of zipped release from password protected website. || biopax || Uniprot || updated periodically || 249 Pathways  || available in biopax level 2 and level 3 ||
|| Reactome || scripted grab of zipped release from website || biopax || Uniprot || updated release ||  1117 pathways (release 37) ||  No way of getting version of release from biopax file ||
|| GO || scripted grab from EBI ftp site (human) || GAF || Uniprot || released once a month || 13,034 no GO IEA <<BR>> 15,181 with GO IEA  ||  source is direct from original curator of annotations ||
|| msigdb - c3 <<BR>> Specialty GMTs <<BR>> mirs, transcription factors || grab from Msigdb || gmt || Entrez gene || sporadically || 221 miRs <<BR>> 616 TFs || ||
+|| '''Source''' || '''File Origin''' || '''File Type''' || '''ID extracted''' || '''Frequency source is updated''' ||  '''Number of pathways''' ||
|| [[http://www.genome.jp/kegg/|KEGG]]^[[#ref1|1]]^ || KEGG ftp site (July 2011) || GMT || Symbol ||  static as of July 1, 2011 || 236 ||
|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c2]]^[[#ref2|2]]^ <<BR>> (other + Biocarta) || manual download from Msigdb || GMT || Entrez gene || sporadically ||  Biocarta - 217<<BR>> Other - 47 ||
|| [[http://pid.nci.nih.gov/|NCI]]^[[#ref3|3]]^ || scripted download of zipped release from website || BioPAX || Entrez gene || sporadically || 219 pathways ||
|| IOB || received directly from IOB - static (July 2011) || BioPAX || Entrez gene || sporadically  || 35 pathways -  <<BR>> 10 are the same as !CellMap,<<BR>> 1 is the same as !NetPath||
|| [[http://www.netpath.org/browse/|NetPath]]^[[#ref4|4]]^ || scripted download of files numbered 1-25 || BioPAX || Entrez gene || static ||  25 pathways - <<BR>> 12 are cancer pathways (10 are !CellMap) <<BR>> 13 are immunity pathways ||
|| [[http://humancyc.org/|HumanCyc]]^[[#ref5|5]]^ || scripted download of zipped release from password protected website. || BioPAX || !UniProt || updated periodically || 249 Pathways  ||
|| [[http://www.reactome.org/ReactomeGWT/entrypoint.html|Reactome]]^[[#ref6|6]]^ || scripted download of zipped release from website || BioPAX || !UniProt || updated release ||  1117 pathways (release 37) ||
|| [[http://www.ebi.ac.uk/GO/|GO]]^[[#ref7|7]]^ || scripted download from EBI ftp site (human) || GAF || Uniprot || released once a month || 13,034 no GO IEA <<BR>> 15,181 with GO IEA  ||
|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c3]]^[[#ref2|2]]^ <<BR>> Specialty GMTs <<BR>> mirs, transcription factors || manual download from Msigdb || GMT || Entrez gene || sporadically || 221 miRs <<BR>> 616 TFs ||
-Line 26:
+Line 35:
-|| '''Source''' || '''File Origin''' || '''File Type''' || '''ID extracted''' || '''Frequency source is updated''' ||  '''Number of pathwayss''' || '''Notes''' ||
|| Reactome || scripted grab of zipped release from website || biopax || Uniprot || updated release ||  946 pathways (release 37) ||  No way of getting version of release from biopax file ||
|| GO || scripted grab from MGI ftp site (human) || GAF || MGI || released once a month || 14,563 no GO IEA <<BR>> 15,041 with GO IEA  ||  source is direct from original curator of annotations ||
|| KEGG || ''translated from Human using Homologene'' || gmt || Entrezgene ||  static as of July 1, 2011 || 236 || Not available in mouse specific format ||
|| Msigdb - c2|| ''translated from Human using Homologene'' || gmt || Entrez gene || sporadically ||  total 880:<<BR>> Kegg -186<<BR>> Reactome - 430<<BR>> Biocarta - 217<<BR>> Other - 47 || Only need other and Biocarta as all other sources are currently covered ||
|| NCI || ''translated from Human using Homologene'' || gmt || Entrez gene || sporadically || 219 pathways ||   ||
|| IOB || ''translated from Human using Homologene'' || gmt || Entrez gene || sporadically  || 35 pathways -  <<BR>> 10 are the same as !CellMap,<<BR>> 1 is the same as !NetPath|| need biopax pathways fixed so species info is correct but information is still extractable. ||
|| !NetPath || ''translated from Human using Homologene'' || gmt || Entrez gene || static ||  25 pathways - <<BR>> 12 are cancer pathways (10 are !CellMap) <<BR>> 13 are immunity pathways || need biopax pathways fixed so species info is correct but information is still extractable. ||
|| !HumanCyc || ''translated from Human using Homologene'' || gmt || Entrez gene || updated periodically || 249 Pathways  || available as Mousecyc in biopax but when we parsed it we got a fraction of the pathways that are in human so chose to convert the human files instead ||
+|| '''Source''' || '''File Origin''' || '''File Type''' || '''ID extracted''' || '''Frequency source is updated''' ||  '''Number of pathways''' ||
|| [[http://www.reactome.org/ReactomeGWT/entrypoint.html|Reactome]]^[[#ref6|6]]^ || scripted download of zipped release from website || BioPAX || !UniProt || updated release ||  946 pathways (release 37) ||
|| [[http://www.informatics.jax.org/mgihome/GO/project.shtml|GO]]^[[#ref7|7]]^ || scripted download from MGI ftp site (mouse) || GAF || MGI || released once a month || 14,563 no GO IEA <<BR>> 15,041 with GO IEA  ||
|| [[http://www.genome.jp/kegg/|KEGG]]^1^ || ''translated from Human using Homologene'' || GMT || Entrez gene ||  static as of July 1, 2011 || 236 ||
|| [[http://www.broadinstitute.org/gsea/msigdb/index.jsp|Msigdb - c2]]^[[#ref2|2]]^ <<BR>> (other + Biocarta)|| ''translated from Human using Homologene'' || GMT || Entrez gene || sporadically ||  total 880:<<BR>> Kegg -186<<BR>> Reactome - 430<<BR>> Biocarta - 217<<BR>> Other - 47 ||
|| [[http://pid.nci.nih.gov/|NCI]]^[[#ref3|3]]^ || ''translated from Human using Homologene'' || GMT || Entrez gene || sporadically || 219 pathways ||
|| IOB || ''translated from Human using Homologene'' || GMT || Entrez gene || sporadically  || 35 pathways -  <<BR>> 10 are the same as !CellMap,<<BR>> 1 is the same as !NetPath||
|| [[http://www.netpath.org/browse/|NetPath]]^[[#ref4|4]]^ || ''translated from Human using Homologene'' || GMT || Entrez gene || static ||  25 pathways - <<BR>> 12 are cancer pathways (10 are !CellMap) <<BR>> 13 are immunity pathways ||
|| [[http://humancyc.org/|HumanCyc]]^[[#ref5|5]]^ || ''translated from Human using Homologene'' || GMT || Entrez gene || updated periodically || 249 Pathways  ||
-Line 54:
+Line 63:
-  * In each <identifier> directory There are amalgamated gene set files:
    * AllPathways - contains all pathway sources in the Pathways directory
    * GOPathways - contains all GO (mf, bp, cc) and all Pathway sources in the Pathways directory.
+  * In each <identifier> directory There are amalgamated Gene Set files:
    * !AllPathways - contains all pathway sources in the Pathways directory
    * GOPathways - contains all GO (MF, BP, CC) and all Pathway sources in the Pathways directory.
-Line 58:
+Line 67:
-== Creating customized Genesets ==
+== Creating customized Gene Sets ==
-Line 64:
+Line 73:
+== References ==
<<Anchor(ref1)>>
  1.  Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. '''KEGG for integration and interpretation of large-scale molecular data sets.''' Nucleic Acids Res. 2011 Nov 10. PMID: 22080510 <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22080510|Pubmed]]
<<Anchor(ref2)>>
  2. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. '''Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.''' Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. PMID: 16199517 <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/16199517|Pubmed]]
<<Anchor(ref3)>>
  3. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. '''PID: the Pathway Interaction Database.''' Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. PMID: 18832364 <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/18832364|Pubmed]]
<<Anchor(ref4)>>
  4. Kandasamy K, ''et a'' '''NetPath: a public resource of curated signal transduction pathways.'''Genome Biol. 2010 Jan 12;11(1):R3. PMID: 20067622 [[http://www.ncbi.nlm.nih.gov/pubmed/20067622|Pubmed]]
<<Anchor(ref5)>>
  5. Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. '''Computational prediction of human metabolic pathways from the complete human genome.''' Genome Biol. 2005;6(1):R2. Epub 2004 Dec 22. PMID: 15642094 <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/15642094|Pubmed]]
<<Anchor(ref6)>>
  6. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. '''Reactome: a database of reactions, pathways and biological processes''' Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7.  PMID: 21067998 [[http://www.ncbi.nlm.nih.gov/pubmed/21067998|Pubmed]]
<<Anchor(ref7)>>
  7. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. '''Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.''' Nat Genet. 2000 May;25(1):25-9. PMID: 10802651 [[http://www.ncbi.nlm.nih.gov/pubmed/10802651|Pubmed]]